PSI-Blast and PHI-Blast through specification of the service which needs to be performed. #12
Conversation
…commands) service, as stated in http://www.ncbi.nlm.nih.gov/blast/Doc/node53.html#labelSERVICE), can solve the problem concerning PSI-BLAST or PHI-BLAST searches over the Blast.NCBIWWW module. I did some tests to check the veracity of this and I think it worked properly. So, I've just inserted 3 lines of additional comments :). Please give me feed back about this subject. I hope I have helped. Fábio Madeira, MSc fbiomadeira@gmail.com
PSI-Blast and PHI-Blast through specification of the service which needs to be performed.
|
Fábio; |
|
Hi Brad, Tell me if you guys need help updating the Biopython's tutorial and cookbook or so. In fact, I don't know if there is a to do list, but it could be nice if I get my hands on starting a kind of module to study protein coevolution, as its my current topic of research... Greetings |
|
Could you prepare a small example to go in test_NCBI_qblast.py using psi/phi BLAST? I wonder if rps-blast works too... |
|
I will see what I can do :) |
|
Fábio; |
Hi there! I found that specifying the 'Put' or 'Get' (works for both commands) service, as stated in http://www.ncbi.nlm.nih.gov/blast/Doc/node53.html#labelSERVICE, can solve the problem concerning PSI-BLAST or PHI-BLAST searches over the NCBIWWW. I did some tests to check the veracity of this and I think it works properly. I've just inserted 3 lines of additional comments in the code :)
Please give me feed back about this subject. I hope I have helped.
Fábio Madeira, MSc
CENTRIA, FCT/UNL, Portugal
fbiomadeira@gmail.com